parmejohn scRNA-pipeline-UofM issues

parmejohn / scRNA-pipeline-UofM

scRNA-seq Pipeline for Drogemoller and Wright Labs

GNU General Public License v3.0

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change apptainer/singularity file to be hosted on dockerhub

#48 parmejohn opened 15 hours ago
1
allow multiple scRNA-seq datasets to be used as tranfser labels

#47 parmejohn opened 6 days ago
0
Change comparative analyses to only perform compare conditions with the same co-variants

#46 parmejohn closed 2 weeks ago
0
find a way to add co-variants to deseq2 analysis

#45 parmejohn opened 1 month ago
4
Implement CellChat analysis

#44 parmejohn closed 1 month ago
0
Edit GSEA plots to have a minimum amount of genes to find a pathway

#43 parmejohn closed 1 month ago
0
Edit GSEA plots for when only 1 condition is shown

#42 parmejohn closed 1 month ago
0
create stratified boxplots for psupertime density distributions

#41 parmejohn closed 1 month ago
0
Perform pathway analysis on the genes in miloR

#40 parmejohn closed 1 month ago
1
change miloR heatmap to give cluster labelled DEGs

#39 parmejohn closed 1 month ago
1
psupertime: find genes that are differentially changing over time given multiple conditions

#38 parmejohn closed 1 month ago
2
add psupertime analyses

#37 parmejohn closed 1 month ago
0
if main condition is time, how would tempora work?

#36 parmejohn closed 1 month ago
0
Refactor functions

#35 parmejohn opened 2 months ago
0
Control ordering of FDR calculations in DA analyses

#34 parmejohn closed 2 months ago
0
Split DA analysis by main condition and co-conditions

#33 parmejohn closed 2 months ago
0
Add in trajectory line labels

#32 parmejohn closed 2 months ago
0
Add in the number/proportion of cells as bar plots

#31 parmejohn closed 2 months ago
0
Look into overflation (QQ plot)

#30 parmejohn opened 2 months ago
0
Fix whitespaces in report file made

#29 parmejohn closed 3 months ago
0
Add in how many cells were filtered out by identifying doublets

#28 parmejohn closed 3 months ago
0
fix the plotting error in the trajectory analysis

#27 parmejohn closed 3 months ago
0
add an option to increase # of genes considered for slingshot DEG list

#26 parmejohn closed 2 months ago
5
add graph titles and labels where appropiate

#25 parmejohn opened 3 months ago
0
print out DEGs from miloR analysis

#24 parmejohn closed 2 months ago
0
implement NEUROeSTIMator

#23 parmejohn closed 2 months ago
2
create option to feed list of pathways of interest for escape to create geyser

#22 parmejohn closed 2 months ago
0
create a report at the end of the analysis of the different samples, and sanity checks

#21 parmejohn closed 3 months ago
0
create small test dataset for proper development

#20 parmejohn closed 3 months ago
2
add in a way to read multiple conditions to initial read of file in order to use tempora/carry out other analyses

#19 parmejohn closed 2 months ago
1
conservedmarkers error '# Error in `levels<-`(`*tmp*`, value = as.character(levels))'

#18 parmejohn closed 3 months ago
1
add different batch correction options

#17 parmejohn closed 3 months ago
1
make sure R scripts dont have to depend on working directory in order to source properly

#16 parmejohn closed 3 months ago
2
random misnamed gene name in DA analysis

#15 parmejohn closed 3 months ago
4
Change GSEA databases to only account for GO:BP

#14 parmejohn closed 3 months ago
1
print out plot in DA analysis for finding optimal K value per number of samples

#13 parmejohn opened 3 months ago
1
change species arguement to be non-case sensitive

#12 parmejohn opened 3 months ago
0
top3 markers heatmap needs to be downsampled/changed

#11 parmejohn closed 3 months ago
1
create a DEG comparison for the main condition in slingshot analysis

#10 parmejohn closed 2 months ago
3
refactor nextflow piplin into modules

#9 parmejohn closed 3 months ago
0
add tempora analysis

#8 parmejohn closed 1 month ago
3
change density of qc plots

#7 parmejohn closed 3 months ago
0
add in more caution and warnings during/after runtime

#6 parmejohn opened 4 months ago
1
if a certain amount of cells are removed during qc -> stop analysis

#5 parmejohn closed 3 months ago
0
Use clustree to find optimal resolution

#4 parmejohn closed 2 months ago
2
Replace normalization, scaling, and other with scTransform

#3 parmejohn opened 4 months ago
1
Add unit testing

#2 parmejohn closed 3 months ago
1
Add in Ensemble to gene symbol conversion

#1 parmejohn closed 3 months ago
1